单基因座和多基因座全基因组关联研究揭示了与棉花幼苗低磷胁迫相关的新基因组区域。

Single- and Multi-Locus GWAS Unravels Novel Genomic Regions Related to Low-Phosphate Stress in Cotton Seedlings.

作者信息

Wei Xianxu, Yao Siyu, Di Jiangnuo, Guan Jiaxin, Wang Aohan, Yang Jie, Zhang Luyao, Liu Yang, Liang Mengyao, Niu Zhihao, Zhang Xuan, Xue Jiarui, Shen Mengxue, Li Lin, Su Yao, Sun Zhengwen

机构信息

State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China.

North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China.

出版信息

Plants (Basel). 2025 Jun 12;14(12):1803. doi: 10.3390/plants14121803.

DOI:10.3390/plants14121803

PMID:40573790

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12196663/

Abstract

Phosphorus (P) is an essential nutrient for plant growth, and low-phosphorus (LP) stress significantly limits cotton productivity. Here, we conducted single- and multi-locus genome-wide association studies (GWASs) on four LP-related traits using 419 upland cotton ( L.) accessions genotyped with 2.97 million single-nucleotide polymorphisms (SNPs). Phenotypic analysis reveals substantial variation under LP stress, with LP-SDW showing the highest coefficient of variation (33.69%). The GWASs identified thousands of significant SNPs, including pleiotropic loci associated with multiple traits. Chromosomes A08, D09, and D12 harbored novel associated signals. Multi-locus models significantly enhanced detection sensitivity, identifying 123 SNPs undetected by single-locus approaches. Functional annotations prioritized six candidate genes near associated SNPs, including GhM_A08G1315 (remorin protein) and GhM_D06G1152 (carotenoid cleavage dioxygenase), whose LP-induced expression patterns were validated by qRT-PCR. These genes are implicated in membrane signaling, root architecture modulation, and hormone metabolism. Our findings provide novel genetic insights into LP tolerance and establish a foundation for breeding phosphorus-efficient varieties through marker-assisted selection in cotton.

摘要

磷（P）是植物生长必需的营养元素，低磷（LP）胁迫显著限制棉花产量。在此，我们利用419份陆地棉种质材料，通过297万个单核苷酸多态性（SNP）进行基因分型，对四个与低磷相关的性状开展了单基因座和多基因座全基因组关联研究（GWAS）。表型分析显示，在低磷胁迫下存在显著变异，其中低磷胁迫下地上部干重（LP-SDW）的变异系数最高（33.69%）。GWAS鉴定出数千个显著的SNP，包括与多个性状相关的多效性位点。A08、D09和D12染色体含有新的关联信号。多基因座模型显著提高了检测灵敏度，鉴定出单基因座方法未检测到的123个SNP。功能注释确定了关联SNP附近的6个候选基因，包括GhM_A08G1315（类remorin蛋白）和GhM_D06G1152（类胡萝卜素裂解双加氧酶），其低磷诱导表达模式通过qRT-PCR得到验证。这些基因与膜信号传导、根系结构调控和激素代谢有关。我们的研究结果为棉花耐低磷提供了新的遗传见解，并为通过标记辅助选择培育磷高效品种奠定了基础。